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204 lines (190 loc) · 6.92 KB
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#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <assert.h>
#include <zlib.h>
#include "kommon.h"
#include "mbpriv.h"
#include "ketopt.h"
int main_index(int argc, char *argv[]);
int main_map(int argc, char *argv[]);
int main_mem(int argc, char *argv[]);
int main_fa2bit(int argc, char *argv[]);
int main_raw2bwt(int argc, char *argv[]);
int main_genraw(int argc, char *argv[]);
int main_genbwt(int argc, char *argv[]);
int main_gensa(int argc, char *argv[]);
int main_getref(int argc, char *argv[]);
int main_fastmap(int argc, char *argv[]);
int main_bench(int argc, char *argv[]);
static int usage(FILE *fp, int is_long)
{
fprintf(fp, "Usage: minibwa <command> <arguments>\n");
fprintf(fp, "Commands:\n");
if (is_long) {
fprintf(fp, " General:\n");
fprintf(fp, " index index reference FASTA\n");
fprintf(fp, " map read alignment\n");
fprintf(fp, " mem legacy bwa-mem CLI (not recommended)\n");
fprintf(fp, " version print the version number\n");
fprintf(fp, " Separate indexing routines:\n");
fprintf(fp, " fa2bit convert FASTA to the long-2bit format\n");
fprintf(fp, " genraw generate BWT from pac with the BWT-SW algorithm\n");
fprintf(fp, " raw2bwt recode bwtgen raw BWT\n");
fprintf(fp, " gensa generate sampled SA from BWT\n");
fprintf(fp, " genbwt generate BWT+SSA from long-2bit with libsais\n");
fprintf(fp, " Debugging:\n");
fprintf(fp, " bench performance evaluation\n");
fprintf(fp, " fastmap test seeding strategies\n");
fprintf(fp, " getref get the reference genome from .l2b\n");
fprintf(fp, " Help:\n");
fprintf(fp, " --help print this help message\n");
} else {
fprintf(fp, " index index reference FASTA\n");
fprintf(fp, " map read alignment\n");
fprintf(fp, " mem legacy bwa-mem CLI (not recommended)\n");
fprintf(fp, " version print the version number\n");
}
return fp == stdout? 0 : 1;
}
int main(int argc, char *argv[])
{
int ret = 0;
kom_realtime();
if (argc == 1) return usage(stdout, 0);
else if (strcmp(argv[1], "index") == 0) ret = main_index(argc-1, argv+1);
else if (strcmp(argv[1], "map") == 0) ret = main_map(argc-1, argv+1);
else if (strcmp(argv[1], "mem") == 0) ret = main_mem(argc-1, argv+1);
else if (strcmp(argv[1], "fa2bit") == 0) ret = main_fa2bit(argc-1, argv+1);
else if (strcmp(argv[1], "genraw") == 0) ret = main_genraw(argc-1, argv+1);
else if (strcmp(argv[1], "raw2bwt") == 0) ret = main_raw2bwt(argc-1, argv+1);
else if (strcmp(argv[1], "genbwt") == 0) ret = main_genbwt(argc-1, argv+1);
else if (strcmp(argv[1], "gensa") == 0) ret = main_gensa(argc-1, argv+1);
else if (strcmp(argv[1], "getref") == 0) ret = main_getref(argc-1, argv+1);
else if (strcmp(argv[1], "bench") == 0) ret = main_bench(argc-1, argv+1);
else if (strcmp(argv[1], "fastmap") == 0) ret = main_fastmap(argc-1, argv+1);
else if (strcmp(argv[1], "--help") == 0) return usage(stdout, 1);
else if (strcmp(argv[1], "version") == 0) {
printf("%s\n", MB_VERSION);
return 0;
} else {
fprintf(stderr, "ERROR: unknown command '%s'\n", argv[1]);
return 1;
}
if (kom_verbose >= 3 && argc > 2 && ret == 0) {
int i;
fprintf(stderr, "[M::%s] Version: %s\n", __func__, MB_VERSION);
fprintf(stderr, "[M::%s] CMD:", __func__);
for (i = 0; i < argc; ++i)
fprintf(stderr, " %s", argv[i]);
fprintf(stderr, "\n[M::%s] Real time: %.3f sec; CPU: %.3f sec; Peak RSS: %.3f GB\n", __func__, kom_realtime(), kom_cputime(), kom_peakrss() / 1024.0 / 1024.0 / 1024.0);
}
return 0;
}
static int usage_getref(FILE *fp)
{
fprintf(fp, "Usage: minibwa getref <ref.l2b>\n");
return fp == stdout? 0 : 1;
}
int main_getref(int argc, char *argv[])
{
uint64_t i, j;
l2b_t *l2b;
if (argc == 1) return usage_getref(stderr);
l2b = l2b_load(argv[1]);
assert(l2b);
for (i = 0; i < l2b->n_ctg; ++i) {
const l2b_ctg_t *ctg = &l2b->ctg[i];
uint8_t *seq;
printf(">%s\n", ctg->name);
seq = kom_malloc(uint8_t, ctg->len);
l2b_getseq(l2b, i, 0, ctg->len, seq);
for (j = 0; j < ctg->len; ++j) seq[j] = "ACGTN"[seq[j]];
fwrite(seq, 1, j, stdout);
fputc('\n', stdout);
free(seq);
}
return 0;
}
typedef enum { MB_BENCH_2A, MB_BENCH_SA, MB_BENCH_MSA } mb_bench_type_t;
static int usage_bench(FILE *fp, int intv)
{
fprintf(fp, "Usage: minibwa bench [options] <in.mbw>\n");
fprintf(fp, "Options:\n");
fprintf(fp, " -b STR type: 2a, sa or msa [2a]\n");
fprintf(fp, " -n NUM number of data points [1m]\n");
fprintf(fp, " -v INT interval size for msa [%d]\n", intv);
fprintf(fp, " -p print results for each data point\n");
fprintf(fp, " -1 use unbatched sa for msa\n");
fprintf(fp, " --help print this help message\n");
return fp == stdout? 0 : 1;
}
int main_bench(int argc, char *argv[])
{
mb_bench_type_t type = MB_BENCH_2A;
uint64_t x = 11, cs = 1;
int64_t i, n = 1000000;
int c, print_val = 0, use_single = 0, intv = 20;
mb_bwt_t *bwt;
ketopt_t o = KETOPT_INIT;
double t;
static ko_longopt_t long_opts[] = {
{ "help", ko_no_argument, 901 },
{ 0, 0, 0 }
};
while ((c = ketopt(&o, argc, argv, 1, "pn:b:v:1", long_opts)) >= 0) {
if (c == 'n') n = kom_parse_num(o.arg, 0);
else if (c == 'p') print_val = 1;
else if (c == '1') use_single = 1;
else if (c == 'v') intv = atoi(o.arg);
else if (c == 'b') {
if (strcmp(o.arg, "2a") == 0) type = MB_BENCH_2A;
else if (strcmp(o.arg, "sa") == 0) type = MB_BENCH_SA;
else if (strcmp(o.arg, "msa") == 0) type = MB_BENCH_MSA;
else kom_assert(0, "unknown type");
}
else if (c == 901) return usage_bench(stdout, intv);
}
if (argc - o.ind < 1) return usage_bench(stderr, intv);
bwt = mb_bwt_load(argv[o.ind]);
t = kom_cputime();
if (type == MB_BENCH_2A) {
for (i = 0; i < n; ++i) {
uint64_t k = kom_splitmix64(&x) % bwt->seq_len;
uint64_t l = kom_splitmix64(&x) % bwt->seq_len;
uint64_t cntk[4], cntl[4];
mb_bwt_rank2a(bwt, k, l, cntk, cntl);
cs = cs * cntk[1] + cntl[0];
if (print_val) printf("%ld\n", (long)cntk[1]);
}
} else if (type == MB_BENCH_SA) {
for (i = 0; i < n; ++i) {
uint64_t s, k = kom_splitmix64(&x) % bwt->seq_len;
s = mb_bwt_sa(bwt, k);
cs = cs * 0xbf58476d1ce4e5b9ULL ^ s;
if (print_val) printf("%ld\n", (long)s);
}
} else if (type == MB_BENCH_MSA) {
for (i = 0; i < n; ++i) {
uint64_t j, xor = 0, k = kom_splitmix64(&x) % bwt->seq_len;
uint64_t l = k + intv < bwt->seq_len? k + intv : bwt->seq_len;
if (use_single) {
for (j = k; j < l; ++j) {
uint64_t s = mb_bwt_sa(bwt, j);
xor ^= s;
}
} else {
uint64_t sa[intv], n_sa = l - k;
for (j = 0; j < n_sa; ++j) sa[j] = k + j;
mb_bwt_sa_batch(0, bwt, l - k, sa);
for (j = 0; j < n_sa; ++j) xor ^= sa[j];
}
cs = cs * 0xbf58476d1ce4e5b9ULL ^ xor;
if (print_val) printf("%ld\n", (long)xor);
}
}
fprintf(stderr, "checksum = %lx\n", (unsigned long)cs);
fprintf(stderr, "t = %.3f\n", kom_cputime() - t);
mb_bwt_destroy(bwt);
return 0;
}